Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

The behavior of ice under extreme conditions undergoes the change of intermolecular binding patterns and leads to the structural phase transitions, which are needed for modeling the convection and internal structure of the giant planets and moons of the solar system as well as H2O-rich exoplanets. Such extreme conditions limit the structural explorations in laboratory but open a door for the theoretical study. The ice phases IX and XIII are located in the high pressure and low temperature region of the phase diagram. However, to the best of our knowledge, the phase transition boundary between these two phases is still not clear. In this work, based on the second-order Møller–Plesset perturbation (MP2) theory, we theoretically investigate the ice phases IX and XIII and predict their structures, vibrational spectra and Gibbs free energies at various extreme conditions, and for the first time confirm that the phase transition from ice IX to XIII can occur around 0.30 GPa and 154 K. The proposed work, taking into account the many-body electrostatic effect and the dispersion interactions from the first principles, opens up the possibility of completing the ice phase diagram and provides an efficient method to explore new phases of molecular crystals.

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Organic crystal polymorphism: a benchmark for dispersion-corrected mean-field electronic structure methods

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520616007885 ◽

2016 ◽

Vol 72 (4) ◽

pp. 502-513 ◽

Cited By ~ 35

Author(s):

Jan Gerit Brandenburg ◽

Stefan Grimme

Keyword(s):

Quantum Chemical ◽

Structure Prediction ◽

Density Functional ◽

Vibrational Energy ◽

Dispersion Interactions ◽

Many Body ◽

Minimal Basis ◽

Blind Test ◽

Semi Empirical ◽

The Impact

We analyze the energy landscape of the sixth crystal structure prediction blind test targets with variousfirst principlesandsemi-empiricalquantum chemical methodologies. A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical methods based on the blind test target crystals is presented. We focus on different means to include London dispersion interactions within the density functional theory (DFT) framework. We show the impact of pairwise dispersion corrections like the semi-empirical D2 scheme, the Tkatchenko–Scheffler (TS) method, and the density-dependent dispersion correction dDsC. Recent methodological progress includes higher-order contributions in both the many-body and multipole expansions. We use the D3 correction with Axilrod–Teller–Muto type three-body contribution, the TS based many-body dispersion (MBD), and the nonlocal van der Waals density functional (vdW-DF2). The density functionals with D3 and MBD correction provide an energy ranking of the blind test polymorphs in excellent agreement with the experimentally found structures. As a computationally less demanding method, we test our recently presented minimal basis Hartree–Fock method (HF-3c) and a density functional tight-binding Hamiltonian (DFTB). Considering the speed-up of three to four orders of magnitudes, the energy ranking provided by the low-cost methods is very reasonable. We compare the computed geometries with the corresponding X-ray data where TPSS-D3 performs best. The importance of zero-point vibrational energy and thermal effects on crystal densities is highlighted.

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Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

Angewandte Chemie ◽

10.1002/ange.201301938 ◽

2013 ◽

Vol 125 (26) ◽

pp. 6761-6764 ◽

Cited By ~ 3

Author(s):

Noa Marom ◽

Robert A. DiStasio ◽

Viktor Atalla ◽

Sergey Levchenko ◽

Anthony M. Reilly ◽

...

Keyword(s):

Molecular Crystal ◽

Dispersion Interactions ◽

Many Body ◽

Crystal Polymorphism

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Many-body dispersion interactions for periodic systems based on maximally localized Wannier functions: Application to graphene/water systems

physica status solidi (b) ◽

10.1002/pssb.201552236 ◽

2015 ◽

Vol 253 (2) ◽

pp. 308-313 ◽

Cited By ~ 4

Author(s):

Pouya Partovi-Azar ◽

Thomas D. Kühne

Keyword(s):

Water Systems ◽

Periodic Systems ◽

Dispersion Interactions ◽

Many Body ◽

Wannier Functions

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Quantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions

Science Advances ◽

10.1126/sciadv.aax0024 ◽

2019 ◽

Vol 5 (12) ◽

pp. eaax0024 ◽

Cited By ~ 11

Author(s):

Martin Stöhr ◽

Alexandre Tkatchenko

Keyword(s):

Density Functional ◽

Van Der Waals ◽

Tight Binding ◽

Quantum Mechanical ◽

Dispersion Interactions ◽

Many Body ◽

Biomolecular Systems ◽

Range Interaction ◽

Factors Affecting ◽

Quantum Mechanical Approach

Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions—the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In contrast to commonly used pairwise approaches, many-body effects substantially decrease the relative stability of native states in the absence of water. Upon solvation, the protein-water dispersion interaction counteracts this effect and stabilizes native conformations and transition states. These observations arise from the highly delocalized and collective character of the interactions, suggesting a remarkable persistence of electron correlation through aqueous environments and providing the basis for long-range interaction mechanisms in biomolecular systems.

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Structure and Stability of Molecular Crystals with Many Body Dispersion Inclusive Density Functional Tight Binding

10.26434/chemrxiv.5662351.v1 ◽

2017 ◽

Author(s):

Majid Mortazavi ◽

Jan Gerit Brandenburg ◽

Reinhard J. Maurer ◽

Alexandre Tkatchenko

Keyword(s):

Structure Prediction ◽

Density Functional ◽

Materials Science ◽

Tight Binding ◽

Molecular Crystals ◽

Dispersion Interactions ◽

Many Body ◽

Structure And Stability ◽

Inclusive Density ◽

Benchmark Database

<pre>Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semi-empirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speed-ups. Here, we combine the Tkatchenko-Scheffler van-der-Waals method (TS) and the many body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speed-up of up to 3000 times compared to a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction. </pre>

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Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.14.26 ◽

2018 ◽

Vol 14 ◽

pp. 381-388 ◽

Cited By ~ 4

Author(s):

Ido Azuri ◽

Anna Hirsch ◽

Anthony M Reilly ◽

Alexandre Tkatchenko ◽

Shai Kendler ◽

...

Keyword(s):

Density Functional ◽

Terahertz Spectroscopy ◽

Chemical Change ◽

Molecular Solids ◽

Dispersion Interactions ◽

Many Body ◽

Functional Theory ◽

Terahertz Spectrum ◽

Intramolecular Vibrations ◽

Good Agreement

We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene. Very good agreement with experimental data is found when using density functional theory that includes Tkatchenko–Scheffler pair-wise dispersion interactions. Furthermore, we show that for these polymorphs the theoretical results are only weakly affected by many-body dispersion contributions. The absence of dispersion interactions, however, causes sizable shifts in vibrational frequencies and directly affects the spatial character of the vibrational modes. Mode assignment allows for a distinction between the contributions of the monoclinic and orthorhombic polymorphs and shows that modes in the range from 0 to ca. 3.3 THz comprise both inter- and intramolecular vibrations, with the former dominating below ca. 1.5 THz. We also find that intramolecular contributions primarily involve the nitro and methyl groups. Finally, we present a prediction for the terahertz spectrum of 1,3,5-trinitrobenzene, showing that a modest chemical change leads to a markedly different terahertz spectrum.

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